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Hubinský M, Hobza R, Starczak M, Gackowski D, Kubát Z, Janíček T, Horáková L, Rodriguez Lorenzo JL. Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3849-3861. [PMID: 38652039 PMCID: PMC11233409 DOI: 10.1093/jxb/erae178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.
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Affiliation(s)
- Marcel Hubinský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marta Starczak
- Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lucie Horáková
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jose Luis Rodriguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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2
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Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210222. [PMID: 35306896 PMCID: PMC8935305 DOI: 10.1098/rstb.2021.0222] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or brings XY male expression back to its ancestral level. Here, we review work on DC in plants, which started as early as the late 1960s with cytological approaches. The use of transcriptomics fired a controversy as to whether DC existed in plants. Further work revealed that various plants exhibit partial DC, including a few species with young and homomorphic sex chromosomes. We are starting to understand the mechanisms responsible for DC in some plants, but in most species, we lack the data to differentiate between global and gene-by-gene DC. Also, it is unknown why some species evolve many dosage compensated genes while others do not. Finally, the forces that drive DC evolution remain mysterious, both in plants and animals. We review the multiple evolutionary theories that have been proposed to explain DC patterns in eukaryotes with XY or ZW sex chromosomes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Aline Muyle
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France
| | - Gabriel A B Marais
- Laboratoire 'Biométrie et Biologie Evolutive', CNRS/Université Lyon 1, Lyon, France.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno, Czech Republic
| | - Thomas Lenormand
- CEFE, University of Montpellier, CNRS, EPHE, IRD, Montpellier, France
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3
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Kobayashi T, Takahashi M, Nishijima R, Sugiyama R, Ishii K, Kawano S, Kazama Y. Effective Chromosomal Preparation Protocol for the Dioecious Plant Silene latifolia. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Taiki Kobayashi
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Masako Takahashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Ryo Nishijima
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Ryuji Sugiyama
- Botanical Garden, Faculty of Agriculture, Tokyo University of Agriculture
| | - Kotaro Ishii
- Nishina Center for Accelerator-Based Science, RIKEN
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Yusuke Kazama
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
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Muyle A, Bachtrog D, Marais GAB, Turner JMA. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200124. [PMID: 33866802 DOI: 10.1098/rstb.2020.0124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Aline Muyle
- University of California Irvine, Irvine, CA 92697, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, F-69622 Villeurbanne, France.,LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Portugal
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5
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Kalinka A, Achrem M. The distribution pattern of 5-methylcytosine in rye (Secale L.) chromosomes. PLoS One 2020; 15:e0240869. [PMID: 33057421 PMCID: PMC7561101 DOI: 10.1371/journal.pone.0240869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/04/2020] [Indexed: 12/02/2022] Open
Abstract
The rye (Secale L.) genome is large, and it contains many classes of repetitive sequences. Secale species differ in terms of genome size, heterochromatin content, and global methylation level; however, the organization of individual types of sequences in chromosomes is relatively similar. The content of the abundant subtelomeric heterochromatin fraction in rye do not correlate with the global level of cytosine methylation, hence immunofluorescence detection of 5-methylcytosine (5-mC) distribution in metaphase chromosomes was performed. The distribution patterns of 5-methylcytosine in the chromosomes of Secale species/subspecies were generally similar. 5-methylcytosine signals were dispersed along the entire length of the chromosome arms of all chromosomes, indicating high levels of methylation, especially at retrotransposon sequences. 5-mC signals were absent in the centromeric and telomeric regions, as well as in subtelomeric blocks of constitutive heterochromatin, in each of the taxa studied. Pericentromeric domains were methylated, however, there was a certain level of polymorphism in these areas, as was the case with the nucleolus organizer region. Sequence methylation within the region of the heterochromatin intercalary bands were also demonstrated to be heterogenous. Unexpectedly, there was a lack of methylation in rye subtelomeres, indicating that heterochromatin is a very diverse fraction of chromatin, and its epigenetic regulation or potential influence on adjacent regions can be more complex than has conventionally been thought. Like telomeres and centromeres, subtelomeric heterochromatin can has a specific role, and the absence of 5-mC is required to maintain the heterochromatin state.
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Affiliation(s)
- Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
- * E-mail:
| | - Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, Poland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, Poland
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6
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Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes (Basel) 2020; 11:E787. [PMID: 32668777 PMCID: PMC7397054 DOI: 10.3390/genes11070787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 01/17/2023] Open
Abstract
About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the >1300 sex-linked genes studied, maximum X-Y divergence was 0.13-0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.
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Affiliation(s)
- Cécile Fruchard
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - Hélène Badouin
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
| | - David Latrasse
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Ravi S. Devani
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Aline Muyle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA;
| | - Bénédicte Rhoné
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
- Institut de Recherche pour le Développement (IRD), Université Montpellier, DIADE, F-34394 Montpellier, France
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany;
| | - Anjan K. Banerjee
- Biology Division, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India;
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris Saclay (IPS2), University of Paris Saclay, 91405 Orsay, France; (D.L.); (R.S.D.); (A.B.)
| | - Gabriel A. B. Marais
- Laboratoire de Biométrie et Biologie Evolutive (LBBE), UMR5558, Université Lyon 1, 69622 Villeurbanne, France; (C.F.); (H.B.); (B.R.)
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7
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Zhou Y, Lu Y, Cheng J, Xu Y. Highly uniform in-situ cell electrotransfection of adherent cultures using grouped interdigitated electrodes. Bioelectrochemistry 2019; 132:107435. [PMID: 31855831 DOI: 10.1016/j.bioelechem.2019.107435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/23/2019] [Accepted: 11/24/2019] [Indexed: 02/05/2023]
Abstract
Cell electrotransfection is an effective approach for transferring exogenous molecules into living cells by electric stimulation. The existing in-situ electrotransfection micro-devices for adherent cells exhibit the drawbacks of low transfection efficiency and low cell viability. An important reason for these drawbacks is the unequal exposure of cells to the electric field. It was found that cells growing directly below the energized electrodes experience a much lower electric field intensity when compared to the cells growing below the spacing area of the electrodes, resulting in low transfection with a strip-like pattern. Therefore, a new strategy for the in-situ electrotransfection of adherent cells growing in a standard 12-well plate is proposed in this study. By sequentially energizing electrodes arranged in a nested and non-contact manner, the cells were exposed to an overall equal intensity of the electric field, and thus a higher efficiency of transfection was achieved. The seven cell lines transfected using this method exhibited high transfection efficiency and high cell viability, demonstrating the potential for studying gene function.
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Affiliation(s)
- Yicen Zhou
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ying Lu
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jing Cheng
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China; Center for Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.
| | - Youchun Xu
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing 100084, China; National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, China.
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8
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Bačovský V, Houben A, Kumke K, Hobza R. The distribution of epigenetic histone marks differs between the X and Y chromosomes in Silene latifolia. PLANTA 2019; 250:487-494. [PMID: 31069521 DOI: 10.1007/s00425-019-03182-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/03/2019] [Indexed: 05/18/2023]
Abstract
Contrasting patterns of histone modifications between the X and Y chromosome in Silene latifolia show euchromatic histone mark depletion on the Y chromosome and indicate hyperactivation of one X chromosome in females. Silene latifolia (white campion) is a dioecious plant with heteromorphic sex chromosomes (24, XX in females and 24, XY in males), and a genetically degenerated Y chromosome that is 1.4 times larger than the X chromosome. Although the two sex chromosomes differ in their DNA content, information about epigenetic histone marks and evidence of their function are scarce. We performed immunolabeling experiments using antibodies specific for active and suppressive histone modifications as well as pericentromere-specific histone modifications. We show that the Y chromosome is partially depleted of histone modifications important for transcriptionally active chromatin, and carries these marks only in the pseudo-autosomal region, but that it is not enriched for suppressive and pericentromere histone marks. We also show that two of the active marks are specifically enriched in one of the X chromosomes in females and in the X chromosome in males. Our data support recent findings that genetic imprinting mediates dosage compensation of sex chromosomes in S. latifolia.
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Affiliation(s)
- Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, 06466, Germany
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65, Brno, Czech Republic.
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9
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Muyle A, Zemp N, Fruchard C, Cegan R, Vrana J, Deschamps C, Tavares R, Hobza R, Picard F, Widmer A, Marais GAB. Genomic imprinting mediates dosage compensation in a young plant XY system. NATURE PLANTS 2018; 4:677-680. [PMID: 30104649 DOI: 10.1038/s41477-018-0221-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/16/2018] [Indexed: 05/06/2023]
Abstract
Sex chromosomes have repeatedly evolved from a pair of autosomes. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced expression and eventual loss of Y genes1. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes. A diverse set of dosage compensating mechanisms that alleviates these negative effects has been described in animals2-4. However, the early steps in the evolution of dosage compensation remain unknown, and dosage compensation is poorly understood in plants5. Here, we describe a dosage compensation mechanism in the evolutionarily young XY sex determination system of the plant Silene latifolia. Genomic imprinting results in higher expression from the maternal X chromosome in both males and females. This compensates for reduced Y expression in males, but results in X overexpression in females and may be detrimental. It could represent a transient early stage in the evolution of dosage compensation. Our finding has striking resemblance to the first stage proposed by Ohno6 for the evolution of X inactivation in mammals.
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Affiliation(s)
- Aline Muyle
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France.
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Cécile Fruchard
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
| | - Radim Cegan
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Vrana
- Institute of Experimental Botany, Center of the Hana Region for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Raquel Tavares
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
| | - Roman Hobza
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Institute of Experimental Botany, Center of the Hana Region for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Franck Picard
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Gabriel A B Marais
- Laboratoire "Biométrie et Biologie Evolutive", CNRS/Université Lyon 1, Lyon, France
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10
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Affiliation(s)
- Roberta Bergero
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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11
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Bačovský V, Hobza R, Vyskot B. Technical Review: Cytogenetic Tools for Studying Mitotic Chromosomes. Methods Mol Biol 2018; 1675:509-535. [PMID: 29052211 DOI: 10.1007/978-1-4939-7318-7_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Significant advances in chromosome preparation and other techniques have greatly increased the potential of plant cytogenetics in recent years. Increase in longitudinal resolution using DNA extended fibers as well as new developments in imaging and signal amplification technologies have enhanced the ability of FISH to detect small gene targets. The combination of fluorescence in situ hybridization with immunocytochemistry allows the investigation of cell events, chromosomal rearrangements and chromatin features typical for plant nuclei. Chromosome manipulation techniques using microdissection and flow sorting have accelerated the analysis of complex plant genomes. Together, the different cytogenetic approaches are invaluable for the unravelling of detailed structures of plant chromosomes, which are of utmost importance for the study of genome properties, DNA replication and gene regulation. In this technical review, different cytogenetic approaches are discussed for the analysis of plant chromosomes, with a focus on mitotic chromosomes.
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Affiliation(s)
- Václaclav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Boris Vyskot
- Department of Plant Developmental Genetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
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12
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Detection of genome DNA methylation change in spinach induced by 5-azaC. Mol Cell Probes 2014; 28:163-6. [PMID: 24556376 DOI: 10.1016/j.mcp.2014.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/21/2014] [Accepted: 02/10/2014] [Indexed: 01/07/2023]
Abstract
DNA methylation has been implicated in the regulation of gene expression, genome imprinting, and chromatin remodeling in eukaryotes. In this study, we analyzed possible alterations in levels and patterns of cytosine methylation in male and female spinach plants after treatment with demethylation agent 5-azacytidine (5-azaC) using two methods: (1) direct determination of 5-methylcytidine (5 mC) amounts in genomic DNA by high-performance liquid chromatography (HPLC) separation and quantification of nucleosides and (2) methylation-sensitive inter-simple sequence repeat (MS-ISSR) technique. HPLC analysis revealed that the DNA methylation events in male and female spinach leaves markedly decreased upon 30 μM 5-azaC treatment, and the methylation level gradually decreased with the increase in 5-azaC concentration. To study the altered DNA methylation patterns in spinach after 5-azaC treatment, untreated and 500 μM 5-azaC-treated samples were analyzed by MS-ISSR assay. A total of 385 informative profiles were resolved using 35 ISSR primer sets. MS-ISSR analysis showed various altered methylation patterns between untreated and 5-azaC-treated spinach plants. These alterations were mainly demethylation events, which were largely consistent with the HPLC results. Both HPLC and MS-ISSR analyses showed that the changes in DNA methylation levels and patterns were similar in male and female spinach leaves, which implies that sex was not the main factor influencing DNA methylation levels and patterns in the vegetative organs of spinach. This study could provide a molecular basis of the altered DNA methylation induced by 5-azaC, and lay a foundation for further investigation of the relationship between methylation and sex determination and development in this dioecious plant spinach.
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Ruffini Castiglione M, Gelati MT, Cremonini R, Frediani M. The intergenic spacer region of the rDNA in Haplopappus gracilis (Nutt.) Gray. PROTOPLASMA 2013; 250:683-689. [PMID: 22948831 DOI: 10.1007/s00709-012-0441-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/24/2012] [Indexed: 06/01/2023]
Abstract
In this paper, we provide further information on the genome organisation of Haplopappus gracilis, one of the six angiosperms showing the lowest chromosome number, i.e. 2n = 4, by determining the nucleotide sequence of the intergenic spacer region of the ribosomal RNA genes and its cytological localization on metaphase chromosomes. DNA sequence analysis reveals the occurring of a product of 4,382 bp in length, characterised by the presence of four blocks of different repeated sequences. Our analysis also evidenced putative promoter regions with three transcription initiation sites for polymerase I, as previously reported in Artemisia absinthium, belonging to the same Asteraceae family. A fluorescent in situ hybridization with the intergenic spacer probe indicates the presence of rDNA genes only in the satellited chromosomes of H. gracilis; besides, differences in the signal intensity between homologous chromosomes were frequently observed, thus suggesting for these chromosome sites the presence of a variable number of rDNA gene copies, even if a divergent chromatin organisation in corresponding regions cannot be ruled out.
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MESH Headings
- Base Sequence
- Chromosome Mapping
- Chromosomes, Plant
- DNA, Ribosomal Spacer/genetics
- Genes, Plant
- Haplopappus/genetics
- Molecular Sequence Annotation
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
- Transcription Initiation Site
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Gschwend AR, Weingartner LA, Moore RC, Ming R. The sex-specific region of sex chromosomes in animals and plants. Chromosome Res 2012; 20:57-69. [PMID: 22105696 DOI: 10.1007/s10577-011-9255-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Our understanding of the evolution of sex chromosomes has increased greatly in recent years due to a number of molecular evolutionary investigations in divergent sex chromosome systems, and these findings are reshaping theories of sex chromosome evolution. In particular, the dynamics of the sex-determining region (SDR) have been demonstrated by recent findings in ancient and incipient sex chromosomes. Radical changes in genomic structure and gene content in the male specific region of the Y chromosome between human and chimpanzee indicated rapid evolution in the past 6 million years, defying the notion that the pace of evolution in the SDR was fast at early stages but slowed down overtime. The chicken Z and the human X chromosomes appeared to have acquired testis-expressed genes and expanded in intergenic regions. Transposable elements greatly contributed to SDR expansion and aided the trafficking of genes in the SDR and its X or Z counterpart through retrotransposition. Dosage compensation is not a destined consequence of sex chromosomes as once thought. Most X-linked microRNA genes escape silencing and are expressed in testis. Collectively, these findings are challenging many of our preconceived ideas of the evolutionary trajectory and fates of sex chromosomes.
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Affiliation(s)
- Andrea R Gschwend
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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15
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Borowska N, Idziak D, Hasterok R. DNA methylation patterns of Brachypodium distachyon chromosomes and their alteration by 5-azacytidine treatment. Chromosome Res 2011; 19:955-67. [PMID: 22076608 PMCID: PMC3228944 DOI: 10.1007/s10577-011-9243-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 01/07/2023]
Abstract
Sequential immunolocalisation of 5-methylcytosine (5-MeC) and fluorescence in situ hybridisation with chromosome-specific BAC clones were performed on Brachypodium distachyon mitotic metaphase chromosomes to determine specific DNA methylation patterns of each chromosome in the complement. In the majority of cells examined, chromosomes Bd4 and Bd5, which bear the loci of 5S and 35S ribosomal DNA, respectively, had characteristic 5-MeC patterns. In contrast, the distribution of 5-MeC along the metacentric chromosome pairs Bd1, Bd2 and Bd3 was more variable. There were numerous differences in distribution of methylated sites between homologous chromosomes as well as between chromosome arms. Some chromosome sites, such as pericentromeric regions, were highly methylated in all chromosomes. Additionally, the influence of a hypomethylating agent, 5-azacytidine, on B. distachyon chromosome methylation patterns was confirmed. It was found that some chromosome pairs underwent demethylation more easily than others, but there was no apparent regularity in demethylation of particular chromosome segments.
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Affiliation(s)
- Natalia Borowska
- Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
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16
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Ruffini Castiglione M, Frediani M, Venora G, Cremonini R. Cytological investigation of Haplopappus gracilis (Nutt.) Gray: 5-methylcytosine-rich regions, fluorochrome banding and chromatin sensitivity to DNase I digestion. PROTOPLASMA 2008; 233:107-113. [PMID: 18615238 DOI: 10.1007/s00709-008-0296-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 10/21/2007] [Indexed: 05/26/2023]
Abstract
Haplopappus gracilis (Nutt.) Gray, one of the five known higher plants with a chromosome number of 2n = 4, was studied from a cytological point of view. The chromosome complement of this species was characterized by means of automated karyotype analysis. Moreover, the DNA methylation pattern and fluorochrome banding were determined and compared with cytological data present in the literature. DNA methylation distribution along metaphase chromosomes involved all chromosome territories evidenced by C-banding. Other methylated bands correlated positively with aceto-orcein-positive heterochromatic portions and/or with late replicating bands and/or fluorochrome bands. Some methylated bands showed differences between homologous chromosomes. These bands belonged partly to certain heterochromatic domains and partly to intercalary sites not defined by other standard banding techniques. Differences between the homologues were also indicated by our DNA content data obtained after DNase I digestion.
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17
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Zluvova J, Georgiev S, Janousek B, Charlesworth D, Vyskot B, Negrutiu I. Early events in the evolution of the Silene latifolia Y chromosome: male specialization and recombination arrest. Genetics 2007; 177:375-86. [PMID: 17603119 PMCID: PMC2013713 DOI: 10.1534/genetics.107.071175] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 06/12/2007] [Indexed: 11/18/2022] Open
Abstract
Understanding the origin and evolution of sex chromosomes requires studying recently evolved X-Y chromosome systems such as those in some flowering plants. We describe Y chromosome deletion mutants of Silene latifolia, a dioecious plant with heteromorphic sex chromosomes. The combination of results from new and previously described deletions with histological descriptions of their stamen development defects indicates the presence of two distinct Y regions containing loci with indispensable roles in male reproduction. We determined their positions relative to the two main sex determination functions (female suppressing and the other male promoting). A region proximal to the centromere on the Y p arm containing the putative stamen promoting sex determination locus includes additional early stamen developmental factors. A medial region of the Y q arm carries late pollen fertility factors. Cytological analysis of meiotic X-Y pairing in one of the male-sterile mutants indicates that the Y carries sequences or functions specifically affecting sex chromosome pairing.
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Affiliation(s)
- Jitka Zluvova
- Department of Plant Developmental Genetics, Institute of Biophysics of the Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
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18
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Abstract
A recent progress in plant molecular biology has led to enormous available data of DNA sequences, including complete nuclear genomes of Arabidopsis, rice, and poplar. On the other hand, in plant species with more complex genomes, containing widespread repetitive sequences, it is important to establish genomic resources that help us to focus on particular part of genomes. Laser technology enables to handle with specific subcellular structures or even individual chromosomes. Here we present a comprehensive protocol to isolate and characterize DNA sequences derived from the sex chromosomes of white campion (Silene latifolia). This dioecious plant has become the most favorite model to study the structure, function, and evolution of plant sex chromosomes due to a large and distinguishable size of both the X and Y chromosomes. The protocol includes a versatile technique to prepare metaphase chromosomes from either germinating seeds or in vitro cultured hairy roots. Such slides can be used for laser chromosome microdissection, fluorescence in situ-hybridization mapping, and immunostaining. Here we also demonstrate some applications of the laser-dissected chromosome template, especially a modified FAST-FISH technique to paint individual chromosomes, and construction and screening of chromosome-specific DNA libraries.
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Affiliation(s)
- Roman Hobza
- Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-612 65 Brno, Czech Republic
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19
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Abstract
DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.
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Affiliation(s)
- B F Vanyushin
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Russia.
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20
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Lu G, Wu X, Chen B, Gao G, Xu K, Li X. Detection of DNA methylation changes during seed germination in rapeseed (Brassica napus). ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11434-005-1191-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Abstract
In mammals, sex is determined by differential inheritance of a pair of dimorphic chromosomes: the gene-rich X chromosome and the gene-poor Y chromosome. To balance the unequal X-chromosome dosage between the XX female and XY male, mammals have adopted a unique form of dosage compensation in which one of the two X chromosomes is inactivated in the female. This mechanism involves a complex, highly coordinated sequence of events and is a very different strategy from those used by other organisms, such as the fruitfly and the worm. Why did mammals choose an inactivation mechanism when other, perhaps simpler, means could have been used? Recent data offer a compelling link between ontogeny and phylogeny. Here, we propose that X-chromosome inactivation and imprinting might have evolved from an ancient genome-defence mechanism that silences unpaired DNA.
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Affiliation(s)
- Khanh D Huynh
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
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22
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Moore RC, Kozyreva O, Lebel-Hardenack S, Siroky J, Hobza R, Vyskot B, Grant SR. Genetic and functional analysis of DD44, a sex-linked gene from the dioecious plant Silene latifolia, provides clues to early events in sex chromosome evolution. Genetics 2003; 163:321-34. [PMID: 12586719 PMCID: PMC1462427 DOI: 10.1093/genetics/163.1.321] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Silene latifolia is a dioecious plant with heteromorphic sex chromosomes. The sex chromosomes of S. latifolia provide an opportunity to study the early events in sex chromosome evolution because of their relatively recent emergence. In this article, we present the genetic and physical mapping, expression analysis, and molecular evolutionary analysis of a sex-linked gene from S. latifolia, DD44 (Differential Display 44). DD44 is homologous to the oligomycin sensitivity-conferring protein, an essential component of the mitochondrial ATP synthase, and is ubiquitously expressed in both sexes. We have been able to genetically map DD44 to a region of the Y chromosome that is genetically linked to the carpel-suppressing locus. Although we have physically mapped DD44 to the distal end of the long arm of the X chromosome using fluorescence in situ hybridization (FISH), DD44 maps to the opposite arm of the Y chromosome as determined by our genetic map. These data suggest that chromosomal rearrangements have occurred on the Y chromosome, which may have contributed to the genetic isolation of the Y chromosome. We discuss the implications of these results with respect to the structural and functional evolution of the S. latifolia Y chromosome.
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Affiliation(s)
- Richard C Moore
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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23
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Janousek B, Matsunaga S, Kejnovsky E, Ziuvova J, Vyskot B. DNA methylation analysis of a male reproductive organ specific gene (MROS1) during pollen development. Genome 2002; 45:930-8. [PMID: 12416626 DOI: 10.1139/g02-052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pollen grains of angiosperm plants represent a good model system for studies of chromatin structure and remodelling factors, but very little is known about the DNA methylation status of particular genes in pollen. In this study, we present an analysis of the DNA methylation patterns of the MROS1 gene, which is expressed in the late phases of pollen development in Silene latifolia (syn. Meladrium album). The genomic sequencing technique revealed similar DNA methylation patterns in leaves, binucleate pollen, and trinucleate pollen. Extremely high DNA methylation levels occurred in the CG dinucleotides of the upstream region (99%), whereas only a low level of CG methylation was observed in the transcribed sequence (7%). Low levels of methylation were also observed in asymmetric sequences (in both regions; 2% methylated). The results obtained in the MROS1 gene are discussed in consequence with the immunohistochemical data showing a hypermethylation of DNA in the vegetative nucleus.
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Affiliation(s)
- Bohuslav Janousek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno.
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24
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Zluvova J, Janousek B, Vyskot B. Immunohistochemical study of DNA methylation dynamics during plant development. JOURNAL OF EXPERIMENTAL BOTANY 2001; 52:2265-73. [PMID: 11709576 DOI: 10.1093/jexbot/52.365.2265] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA methylation represents one of the key processes that play an important role in the transcriptional control of gene expression. The role of cytosine methylation in plant development has been demonstrated by at least three different kinds of evidence: parent-specific expression of some genes in developing seeds, control of flowering time and floral morphogenesis, and correlation with silencing of intrusive DNA sequences (mobile genetic elements and transgenes). In this work global changes in DNA methylation during seed germination and shoot apical meristem development in Silene latifolia have been studied using an indirect immunohistochemical approach. The data presented show that a rapid decrease in global DNA methylation during seed germination occurs first in endosperm tissue and subsequently in the hypocotyl. Using 5-bromo-2'-deoxyuridine pulses, it has been demonstrated that these demethylation events occurred before cell division had begun. In the early post-germination period, a decrease in DNA methylation was detected in cotyledons, also before cell division was observed. Taken together, these results indicate that DNA demethylation takes place in a non-replicative way, probably by an active mechanism. The central zone of the shoot apical meristem remains highly methylated during the whole period of vegetative growth and in this region, only a low cell division activity was found. However, upon the transition of the shoot apical meristem to the floral bud, the meristem both decreased its high methylation status and its cells started to divide. These data indicate that the central zone of the shoot apical meristem can represent a relatively quiescent 'germ-line' which is activated upon flowering to form spores and gametes.
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Affiliation(s)
- J Zluvova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska str. 135, CZ-612 65 Brno, Czech Republic
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25
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Atanassov I, Delichère C, Filatov DA, Charlesworth D, Negrutiu I, Monéger F. Analysis and evolution of two functional Y-linked loci in a plant sex chromosome system. Mol Biol Evol 2001; 18:2162-8. [PMID: 11719565 DOI: 10.1093/oxfordjournals.molbev.a003762] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
White campion (Silene latifolia) is one of the few examples of plants with separate sexes and with X and Y sex chromosomes. The presence or absence of the Y chromosome determines which type of reproductive organs--male or female--will develop. Recently, we characterized the first active gene located on a plant Y chromosome, SlY1, and its X-linked homolog, SlX1. These genes encode WD-repeat proteins likely to be involved in cell proliferation. Here, we report the characterization of a novel Y-linked gene, SlY4, which also has a homolog on the X chromosome, SlX4. Both SlY4 and SlX4 potentially encode fructose-2,6-bisphosphatases. A comparative molecular analysis of the two sex-linked loci (SlY1/SlX1 and SlY4/SlX4) suggests selective constraint on both X- and Y-linked genes and thus that both X- and Y-linked copies are functional. Divergence between SlY4 and SlX4 is much greater than that between the SlY1 and SlX1 genes. These results suggest that, as for human XY-linked genes, the sex-linked plant loci ceased recombining at different times and reveal distinct events in the evolutionary history of the sex chromosomes.
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Affiliation(s)
- I Atanassov
- Laboratoire de Reproduction et Développement des Plantes, Ecole Normale Supérieure Lyon, Lyon, France
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26
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Bernardino J, Lombard M, Niveleau A, Dutrillaux B. Common methylation characteristics of sex chromosomes in somatic and germ cells from mouse, lemur and human. Chromosome Res 2001; 8:513-25. [PMID: 11032321 DOI: 10.1023/a:1009271706488] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
DNA methylation of sex chromosomes was analysed using anti-5-methylcytosine antibodies on metaphase chromosomes of somatic cells from three species: human, lemur and mouse. Germ cells were also studied in male mouse. In female cells (human and mouse), the late replicating X was always the less methylated chromosome. Compared with autosomes, the methylation of both X chromosomes was always lower in fibroblasts than in lymphocytes and the difference was always greater in mouse than in human. In human, mouse and lemur male cells, the labelling of the unique X chromosome was quite similar to that of the early replicating X from female cells. Except for the heterochromatic region of the human Y chromosome, strongly methylated, the overall methylation of the Y chromosome was low. In mouse testicular cells, a variety of DNA methylation patterns was observed according to the cell type and the state of differentiation. Finally, the only structures of sex chromosomes which remain methylated in all conditions correspond to their pseudoautosomal regions.
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Affiliation(s)
- J Bernardino
- Laboratoire d'étude de la Radiosensibilité des Cellules Germinales, Département de Radiobiologie et Radiopathologie, Fontenay-aux-roses, France
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27
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Castilho A, Neves N, Rufini-Castiglione M, Viegas W, Heslop-Harrison JS. 5-Methylcytosine distribution and genome organization in triticale before and after treatment with 5-azacytidine. J Cell Sci 1999; 112 ( Pt 23):4397-404. [PMID: 10564657 DOI: 10.1242/jcs.112.23.4397] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Triticale (2n=6x=42) is a hybrid plant including rye (R) and wheat (A and B) genomes. Using genomic in situ hybridization with rye DNA as a probe, we found the chromosomes of the R genome were not intermixed with the wheat chromosomes in 85% of nuclei. After treatment of seedlings with low doses of the drug 5-azacytidine (5-AC), leading to hypomethylation of the DNA, the chromosomes became intermixed in 60% of nuclei; the next generation showed intermediate organization. These results correlate with previous data showing that expression of R-genome rRNA genes, normally suppressed, is activated by 5-AC treatment and remains partially activated in the next generation. The distribution of 5-methylcytosine (5-mC) was studied using an antibody to 5-mC. Methylation was detected along the lengths of all chromosomes; there were some chromosome regions with enhanced and reduced methylation, but these were not located at consistent positions, nor were there differences between R and wheat genome chromosomes. After 5-AC treatment, lower levels of methylation were detected. After 5-AC treatment, in situ hybridization with rye genomic DNA sometimes showed micronuclei of rye origin and multiple translocations between wheat and rye chromosomes. Genomic DNA was analysed using methylation-sensitive restriction enzymes and, as probes, two rDNA sequences, two tandemly organised DNA sequences from rye (pSc200 and pSc250), and copia and the gypsy group retrotransposon fragments from rye and wheat. DNA extracted immediately after 5-AC treatment was cut more by methylation-sensitive restriction enzymes than DNA from untreated seedlings. Each probe gave a characteristic restriction fragment pattern, but rye- and wheat-origin probes behaved similarly, indicating that hypomethylation was induced in both genomes. In DNA samples from leaves taken 13–41 days after treatment, RFLP (Restriction Fragment Length Polymorphism) patterns were indistinguishable from controls and 5-AC treatments with all probes. Surprising differences in hybridization patterns were seen between DNA from root tips and leaves with the copia-fragment probes.
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Affiliation(s)
- A Castilho
- Karyobiology Group, Dep. of Cell Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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